IMP Reference Guide
2.14.0
The Integrative Modeling Platform
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Support for the mmCIF file format. More...
Support for the mmCIF file format.
IMP has basic support for writing out files in mmCIF format, for deposition in PDB-Dev. mmCIF files are currently generated by creating an IMP.pmi.mmcif.ProtocolOutput class, and attaching it to an IMP.pmi.representation.Representation object, after which any generated models and metadata are collected and output as mmCIF.
Classes | |
class | AsymUnit |
A single asymmetric unit in the system. More... | |
class | Entity |
A single entity in the system. More... | |
class | GMMParser |
Extract metadata from an EM density GMM file. More... | |
class | ProtocolOutput |
Class to encode a modeling protocol as mmCIF. More... | |
Functions | |
def | get_dumpers |
Get custom python-ihm dumpers for writing PMI to from mmCIF. More... | |
def | get_handlers |
Get custom python-ihm handlers for reading PMI data from mmCIF. More... | |
def | read |
Read data from the mmCIF file handle fh . More... | |
def IMP.pmi.mmcif.get_dumpers | ( | ) |
Get custom python-ihm dumpers for writing PMI to from mmCIF.
This returns a list of custom dumpers that can be passed as all or part of the dumpers
argument to ihm.dumper.write(). They add PMI-specific information to mmCIF or BinaryCIF files written out by python-ihm.
def IMP.pmi.mmcif.get_handlers | ( | ) |
Get custom python-ihm handlers for reading PMI data from mmCIF.
This returns a list of custom handlers that can be passed as all or part of the handlers
argument to ihm.reader.read(). They read PMI-specific information from mmCIF or BinaryCIF files read in by python-ihm.
def IMP.pmi.mmcif.read | ( | fh, | |
model_class = ihm.model.Model , |
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format = 'mmCIF' , |
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handlers = [] |
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Read data from the mmCIF file handle fh
.
This is a simple wrapper around ihm.reader.read()
, which also reads PMI-specific information from the mmCIF or BinaryCIF file.